Background: Periodontitis is a multifactorial infection caused by a complex of pathogenic bacterial species that induce the destruction of periodontal structures.Objective:The aim of this study is to evaluate the presence and bacterial load of six periodontal pathogens bacteria, measured at initial visit and after osseous surgery in patients affected by chronic periodontitis and treated between 2005 and 2007.Methods:This cohort study was carried out on a sample of 38 consecutive patients affected by severe chronic periodontitis, diagnosed at baseline on the basis of probing depths equal to 6.68 ± 1.47 mm. On each subject, a microbiological test was performed before periodontal initial therapy and after osseous surgery (one year later). Five compromised teeth were chosen for each patient (the same teeth, before and after surgery), for a total of 190 teeth. Real-time PCR based analysis computed total bacterial load of the samples and quantified six periodontal pathogens: Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Fusobacterium nucleatum and Prevotella intermedia. Data collection was made consulting medical charts.Results:Pocket probing depth reduction after surgery was 4.50 ± 1.54 mm (p=0.0001). The mean number of sites with bleeding at baseline was 2.08 ± 1.17 and 0.58 ± 1.00 after surgery (p=0.001). The mean number of sites with suppuration at baseline was 0.26 ± 0.86 and 0 after surgery (p=0.02). Cell count of each pathogen and total cell count were significantly higher at baseline than after surgery. Almost all bacteria presented a mean percentage reduction equal to that of the total count, except for Aa and Pi, which seemed to show a greater resistance. The difference of bacterial load, both before and after surgery, between smokers and non-smokers was not statistically significant (p<0.05). A statistically significant correlation was detected between pocket probing depth variation and bleeding on probing variation before and after the surgery, controlling for age (r=0.6, p=0.001). No significant correlations were observed between pocket probing depth and bacterial loads, except for Pg (r=0.5, p=0.001), Tf (r=0.6, p=0.001) and Td (r=0.4, p=0.02).Conclusions:Reduction of presence and bacterial load of the examined periodontal pathogens bacteria after osseous surgery, along with periodontal pocket reduction, appeared to be essential to achieve and maintain periodontal stability over years.